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New mechanism of evolution — POOF

Each species has large numbers of unique genes that seem to have magically arisen without any ancestor. Evolutionists are saying they essentially POOFed into existence. These genes are referred to as ORFans or orphan genes. From the Max Plank Institute:

However, with the advent of sequencing of full genomes, it became clear that approximately 20–40% of the identified genes could not be associated with a gene family that was known before. Such genes were originally called ‘orphan’ genesEvolutionary Origin of Orphan Genes

20-40% of the genes discovered cannot be explained by common ancestry or common descent. So what mechanism is left to explain it? Special creation? But evolutionists can’t accept special creation, so they just pretend they’ve made a discovery of a new mechanism of evolution that can work just as well. They haven’t given it a name yet, so let us call it POOF. What is POOF? POOF is the mechanism by which proteins can easily arise out random nucleotide sequences like a poem can emerge out of randomly tossed scrabble letters. I bold one of their euphemisms for the POOF mechanism in the following paragraph:

Orphan genes may have played key roles in generating lineage specific adaptations and could be a continuous source of evolutionary novelties. Their existence suggests that functional ribonucleic acids (RNAs) and proteins can relatively easily arise out of random nucleotide sequences, although these processes still need to be experimentally explored.

😯

The reasoning they use goes like this, “we have all these genes that can’t be explained by slight successive modifications, so they must have arisen spontaneously out of nowhere. Because evolution is fact, this implies evolution can just take random material and create functional systems in a flash. We’ve made a fabulous discovery about the miracles of evolution even though we can’t demonstrate it experimentally.”

Experiments actually refute such assertions, but that won’t stop evolutionists from promoting demonstrably false ideas as some new discovery! And it’s not only the genes but the regulatory mechanisms that poof into existence:

On the other hand, there is now little doubt that new genes have arisen throughout the phylogenetic history and the general model of de novo evolution of genes appears to be well supported by now. However, this also raises several new questions. The foremost one is the question of how new promotors with a defined regulation can arise.

“de novo evolution of genes” is also another euphemism for the POOF mechanism.

But it’s not just the genes and regulatory regions, but also developmental mechanisms that deploy these novelties to create radical new species (like multicellular ones from single cellular ones).

gene lists can be associated with major evolutionary steps, such as the origin of germ layers, or the origin of multicellularity . Interestingly, this approach showed also that younger genes tend to be increasingly more developmentally regulated compared with evolutionary older genes

Not only do the orphan genes emerge, they emerge with the most infrastructure to integrate them into the POOFED species. So genes, proteins, and developmental mechanisms, and new species also POOFED into existence. They sound almost like closet creationists!

The evolutionists conclude, evolution can do far more than we ever supposed because evolution can POOF thousands of genes and regulatory mechanisms into sudden existence rather than through slight successive modifications of an ancestor. What a wonderful discovery.

NOTES

1. Behe, who accepts common descent, is said to have jokingly used the phrase, “puff of smoke” to describe the mechanism that can create irreducible complexity. In internet debates, the phrase got converted to “POOF” to emphasize the magical character of the mechanism. It seems now, evolutionary biologists are seriously resorting to Behe’s POOF mechanism whether they want to admit it or not.

How did Behe arrived at the POOF mechanism which evolutionary biologists are now only discovering?

I lectured at Hillsdale College as part of a week-long lecture series on the intelligent design debate. After Michael Behe’s lecture, some of us pressed him to explain exactly how the intelligent designer created the various “irreducibly complex” mechanisms that cannot–according to Behe–be explained as products of evolution by natural selection. He repeatedly refused to answer. But after a long night of drinking, he finally answered: “A puff of smoke!”

76 Responses to New mechanism of evolution — POOF

” “de novo evolution of genes” is also another euphemism for the POOF mechanism.”
No, its not. They clearly state in the abstract that genes arising “de novo” means arising from non-coding DNA, which is a the majority of your DNA by the way.
Nice job guys.

You know evolution is a really great theory because it will not be hindered by meddlesome falsifiability that drags down all of the weaker theories.

Gee whiz, roughly a third of all the animals’ genes have no trace of common ancestry whatsoever, completely contradicting evolutionary expectations and predictions. But evolution theory thrives under such conditions.

Homology-free ‘de novo’ function of Orphan genes has just become assimilated. Orphans can now be used as evidence for evolution.

Thank goodness for this new research that sheds more light on how evolution is a fact.

Provide for the reader the probability that a random nucleotide sequence of 300 nucleotides will code for a functional protein. Recall we are talking about orphans that have no discernible common ancestor so we can’t just take an existing functional protein and make a slight modification to it, we have to start from scratch.

Provide for the reader your estimate. Feel free to justify how you arrived at that number. You brag about your deep knowledge of biology, so now you’ll have a chance to showcase just how much molecular biology you actually understand.

Why is it too small? If it’s too small, provide a number that you think is right, then provide what you think is a probability.

You boast about all the evidence for evolution, here is your chance to shine and prove there actually is evidence for evolution.

Evolution implies random process can manufacture novel features. So here is your chance to explain how a novel feature can suddenly emerge. Recall, by definition, the orphan is presumed not to have an ancestor and emerged very quickly and not by slow successive variation.

So provide a number that a random nucleotide sequence can yield a protein. Think I’m asking too much, this is exactly what this paper claims (despite the mathematical hurdles):

proteins can relatively easily arise out of random nucleotide sequences

Elsewhere in the paper they point out it was believed based on math, that such orphans can’t arise, but now that we’ve found orphans, they assume there must have been something wrong with the math!

Proteins and Genes, Singletons and Species – Branko Kozuli? PhD. Biochemistry
Excerpt: Horizontal gene transfer is common in prokaryotes but rare in eukaryotes [89-94], so HGT cannot account for (ORFan) singletons in eukaryotic genomes, including the human genome and the genomes of other mammals.,,,
The trend towards higher numbers of (ORFan) singletons per genome seems to coincide with a higher proportion of the eukaryotic genomes sequenced. In other words, eukaryotes generally contain a larger number of singletons than eubacteria and archaea.,,,
That hypothesis – that evolution strives to preserve a protein domain once it stumbles upon it contradicts the power law distribution of domains. The distribution graphs clearly show that unique domains are the most abundant of all domain groups [21, 66, 67, 70, 72, 79, 82, 86, 94, 95], contrary to their expected rarity.,,,
Evolutionary biologists of earlier generations have not anticipated [164, 165] the challenge that (ORFan) singletons pose to contemporary biologists. By discovering millions of unique genes biologists have run into brick walls similar to those hit by physicists with the discovery of quantum phenomena. The predominant viewpoint in biology has become untenable: we are witnessing a scientific revolution of unprecedented proportions.http://vixra.org/pdf/1105.0025v1.pdf
Of Note: Branko Kozulic is on the editorial team of BioComplexityhttp://bio-complexity.org/ojs/.....TeamBio/23

Age doesn’t matter: New genes are as essential as ancient ones – December 2010
Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”http://www.sciencedaily.com/re.....142523.htm

Thank you Frank, that was lovely. Do you have anything else to add?
I realize there are proteins of less than 100 amino acids, but for the purpose of this little chat, I do not want to use an extremely small protein.

AVS: Thank you Frank, that was lovely. Do you have anything else to add?

Sure. Functionality of small proteins and peptides is an important part of the argument.

sal: I was referring to functional proteins, not random amino-acid polymers, or do you not understand the difference?

You’ll need to define functionality as it pertains to your argument. for example plasma proteins contribute to osmolality, binding of protons is also an important function of proteins in maintaining pH homeostasis, and allosteric binding of CO2 (and protons) is an important function of hemoglobins. To think that all function must be catalytic is naive and misses a great deal of what biochemistry is all about.

Here is the quote that acknowledges that math says novel proteins are combinatorially improbable. Yet, because we have orphan genes that were discovered via “the breadth of genomic comparison”, combined with the fact evolution is true, then the combinatorial math must have been wrong!

😯

The de novo evolution model constitutes the largest
conceptual step forward in our understanding of gene
evolution. On the basis of simple combinatorial considerations, it seemed initially very unlikely that functional proteins could arise out of essentially random sequences (Jacob, 1977). However, direct and indirect evidence for de novo evolution has quickly accumulated in the past years, due to the breadth of genomic comparisons that are now available;

If you took random sequences 1200 nt long you’d almost certainly hit an in-frame stop codon. Even if you didn’t, most amino acid sequences aren’t functional (lots of RNA sequence are though.

So it’s unlikely any given random sequences will create a protein.

On the other hand, there aren’t all that many ORFans (10-20% is an ascertainment bias since we go out of our way to sequence species from across the tree of life), and many of them likely do have genes as ancestors (which we can’t detect thanks to elevated evolutionary rates) and others can be explained by gene-loss not gene gain.

So, we probably don’t need to explain all that many de novo genes origins, but it’s silly to pretend functional sequence would just pop into existence willy nilly.

I guess you haven’t gotten to the coursework that covers non-bicarbonate buffering capacity (as measured in slykes) or perhaps even allosteric binding and its importance. Maybe a bit of a venture into the realm of pharmacology and its sister science toxicology would expand your horizons!

Eh I took biochem so I have an idea about some of that, but seriously, your point about the small proteins is moot in this conversation. I wanted to create a hypothetical protein chain and I didn’t want it to be short, its that simple. Cool your jets, we get it, youre gonna be counting pills for the rest of your life mr pharm major =)

If you took random sequences 1200 nt long you’d almost certainly hit an in-frame stop codon. Even if you didn’t, most amino acid sequences aren’t functional (lots of RNA sequence are though.

So it’s unlikely any given random sequences will create a protein.

On the other hand, there aren’t all that many ORFans (10-20% is an ascertainment bias since we go out of our way to sequence species from across the tree of life), and many of them likely do have genes as ancestors (which we can’t detect thanks to elevated evolutionary rates) and others can be explained by gene-loss not gene gain.

So, we probably don’t need to explain all that many de novo genes origins, but it’s silly to pretend functional sequence would just pop into existence willy nilly.

AVS aka newbie almost a biologist: Eh I took biochem so I have an idea about some of that, but seriously, your point about the small proteins is moot in this conversation. I wanted to create a hypothetical protein chain and I didn’t want it to be short, its that simple. Cool your jets, we get it, youre gonna be counting pills for the rest of your life mr pharm major

You can hamstring your argument in any fashion you like, e.g., as wd400 has pointed out.

I think you’ll find that there are a lot of folks out there with advanced degrees in Pharmacology and Toxicology that work in a variety of realms outside of the Walmart pharmacy that don’t involve counting pills….although there is nothing wrong with that!

What about those that deny common descent? As a consequence whole new kinds along with the supporting ecosystems must have poofed into existence!

Great observation! So it makes sense then that all life, if it had been intelligently designed, and specially created — it stands to reason, by inference, that it happened rather fast, maybe on the order of a few days lest those at the top of the food chain starve, thus the creationists may have a little edge over the front-loaded-evolutionists in the ID community.

One way of characterising the difference between ID and evolutionary science is that ID is happy to say the designer took care of the poofery end of story while scientists try to find explanations.

Well, I would simply say that:

a) The emergence of new functional sequences by non design mechanisms against all reasonable odds and against all scientific and empirical credibility is certainly a “poof”: functional order coming out without any explanation. The recent debate with some of your side about the belief in “fluke results” here:

The fact remains, believing that function arises without even a trace of explanation about how it arises is believing in a “poof”.

b) On the other hand, a design explanation is no poof at all. It just means to propose that function arises because a conscious intelligent being inputs purposeful functional order into matter, and that is exactly what we observe in human design.

You will certainly object that in the ID scenario we “poof” the conscious intelligent being into existence. We have debated that, and I have tried to show how that “argument” is inevitably dependent on previous ideological commitments about general worldviews.

But certainly, if we admit that conscious intelligent beings other than humans, and possibly non physical, may exist, then the ID explanation relies on no “poof” at all. The emergence of functional order from conscious representations is no poof: it is an observed fact.

Coin-tosses are not relevant. Evolution takes functional proteins and tries minor variations. It does not randonmly assemble sequences from thin air. Also nobody knows how rich in functional proteins the sequence space of all possible proteins is.

I think we more or less agree on the ID side. Given something that appears to “poof” it is sufficient explanation as far as you are concerned that a designer made it happen that way. There has been attempt of any significance to go beyond that – maybe a bit of informal conjecture about front-loading.

The difference in our accounts is that I would say evolutionary scientists keep on seeking explanations of how things poofed into existence. You may not be satisfied with current explanations – that is beyond my skill to assess – but it is undeniably an area of continuing research with hypotheses and data subject to refutation and confirmation i.e. science.

Coin tosses are absolutely relevant. Random variation is an essential part of the proposed neo darwinian algorithm, and coin tosses are the classic model for random events.

Moreover, minor variations on existing functional proteins are not going to explain how new protein domains and superfamilies arise, which is exactly what we have to explain.

Finally, while it is true that nobody knows exactly how rich in functional proteins the sequence space of all possible proteins is, it is equally true that we know much about that, and nothing of what we know is “darwinian friendly”. I would say that the problem is that darwinists would like to keep that issue as dark as possible, because only that “ignorance” can give them an excuse to go on believing their irrational dogmas, while IDists are absolutely interested in clarifying as soon as possible the point beyond any possible doubt.

It’s perfectly fair that evolutionary scientists “keep on seeking explanations of how things poofed into existence”, trying to give some kind of support to their hypothesis. It is not fair that they pretend to have explanations that they do not have.

It is equally fair that ID scientists keep on seeking facts that support their theory, and explanations of how, when and why new information was inputted into living beings. That is, in making ID science.

It is definitely not fair that you consider science only what is done under the dogmatic ideology of materialist reductionism.

It is equally fair that ID scientists keep on seeking facts that support their theory, and explanations of how, when and why new information was inputted into living beings. That is, in making ID science.

Absolutely it would be fair if they did it. I am not aware of any attempt by any ID “scientist” to seek facts about how, when and why new “information” was inputted into living beings. Can you name one? Indeed how would they set about that task?

(I put the quote marks round scientist and information because I don’t want someone quote mining me to say I accept that ID is science and that information is something you can add like mass or energy.)

I’m out and about and trying to enjoy the sunshine over the weekend but will respond fully when I can get to a proper keyboard. I strongly disagree on your superfamily claim. Have you seen Kirk Durstson’s recent thread?

‘The de novo evolution model constitutes the largest conceptual step forward in our understanding of gene evolution.’ Quoted from Salvatore’s quote in his #16.

‘A conceptual step forward…’ Wow! these guys don’t mess about incrementally, do they? Only modesty, presumably prompted their designation of their discovery of this great de novo poofery as ‘a conceptual step forward’, rather than ‘a conceptual LEAP forward’.

And Barry in his #25:

‘Materialists love “poofery.” I’ve been pointing this out for years:’

They have no choice, really, if they are to carry on with the motley, do they?

Christ has the words of eternal life, but where else shall they go, since poofery has the words of eternal evolution?

No one disagrees with this but has anything but trivial changes ever occurred? This fact which you continually bring up is irrelevant to the debate.

Also nobody knows how rich in functional proteins the sequence space of all possible proteins is.

Apparently there are ways of estimating this. And it appears they are very rare. So rare that it is extremely unlikely that non-cocing sequences would turn into one. Maybe a few but not enough to make a difference.

And then there is the issue of just how the organism would use the new coding section. Where are the instructions that put all the parts together and how would it fit in the new gene to develop new capabilities.

There have been several threads describing these unique genes. Have they identified the proteins in the specific organisms that are coded by these genes and if so how they fit into the operation of the organism?

Interestingly, this approach showed also that younger genes tend to be increasingly more developmentally regulated compared with evolutionary older genes

This sort of answers the question as to whether these genes are expressed but is not even close to a complete answer. If these genes are regulated let alone heavily regulated, they must be expressed somehow in some of the cells. What do they do?

This is just one aspect of the evolution debate. But it is only a small part of the investigation into how complex novelties arose. Meyer’s book begins the discussion about where the debate should be headed, embryo development.

Have they identified the proteins in the specific organisms that are coded by these genes

GREAT QUESTION!

Not always, and to my utter amazement, we haven’t even found the proteins for many of the genes we think aren’t orphans! I found this out when I watch how gene numbers were revised on a daily basis and when Eric Lander mentioned in a paper we need to confirm Gene existence via protein detection!

Complicating this is the huge number of protein isoforms (slightly modified proteins) that come from a few genes through alternative splicing and somatic variation. There are perhaps millions of these proteins coming from 20,000 “gene” sites. What is disturbing is what we get in the popular press as fact and knowledge are actually educated guesses! We could be very different from chimps at the molecular level if the isoforms are different. We just don’t know…

Also, when I heard of immortal DNA, that means that DNA copies from cell to cell are slightly altered. This makes sense in a multicellular organism. How does that affect protein diversification. I don’t know.

I posted this discussion about orpahans as a precursor to reporting on Paul Nelson’s keynote at ICC 2013 on Orphan genes. He’s taken a lot of flak on the topic over the years, made a couple blunders (by his own admission) over the topic, but it looks like so far he is being vindicated.

Apparently protein detection is really hard. I know enzymes can exist in 1 part per million. There are so many biomolecules in an organism, and it is hard to actually find them. Protein coding genes are inferred by the sequences, so there is a lot of work to do.

Some of the retrogene (processed pseudogene) orphans were dismissed until we actually started seeing their products in the human body through cancer research.

For all the embarrassments the YECs have caused for themselves over the years, the new generation of biologists in the YEC community are vindicating themselves and getting quietly published in secular peer reviewed journals. Tomkins is one of them, Sanford (obviously), others — I’ve been asked to keep quiet on. 😉

One way of characterising the difference between ID and evolutionary science is that ID is happy to say the designer took care of the poofery end of story while scientists try to find explanations.

I totally respect that, but what if poof really was the way it happened? Seriously, this raises an interesting question, if an unrepeatable, unobservable poof was the way it happened, how could we scientifically lend credence to such a hypothesis. I’d argue, exactly the way ID proponents and especially creationists are going about the question, criticizing existing OOL and evolutionary mechanisms accepted today and any evolutionary mechanisms that might proposed in the future even in principle.

Evolutionary biologists really don’t like what ID proponents and creationists are doing in trying to falsify evolutionary ideas, but that is exactly the correct scientific approach if one is defending a poof-type hypothesis.

We saw a smaller scale of this in cosmology, and the POOF mechanism got a derogatory name that stuck, namely, “The Big Bang”.

The phrase poof was used at ARN prior to UD. There was a discussion (at ARN I think) that the term got used as a term of derision against ID proponents and the term started being used more frequently against IDists because of Behe’s “puff of smoke” comment.

Poof the Magic Mutant, a-t-g-c
And changed them just by randomness just to see what he could be.
Little Richard Dawkins, loved that rascal Poof.
And wrote him books to appease the kooks, oh what a silly goof!

Oh Poof the Magic Mutant, a-t-g-c
And changed them just by randomness just to see what he could be

Poof the Magic Mutant, a-t-g-c
And changed them just by randomness just to see what he could be

Together they would mutate Poof into a beluga whale
Richard kept a spectroscope trained on Poof’s mutating tail.
Nobel things and atheists bowed whene’er they came
Scientists would lower their flasks when Poof mutated a mane

Oh Poof the Magic Mutant, a-t-g-c
And changed them just by randomness just to see what he could be

Poof the Magic Mutant, a-t-g-c
And changed them just by randomness just to see what he could be

Mutations can’t go on forever, just like little boys
Antennaed wings and giant things doom nature’s mutant ploys
One gray night it happened, natural selection said no more
And Poof that Magic Mutant, mutated one last roar

His head was bent in sorrow, his tears fell like rain
Richard no longer went to write it gave him so much pain
Without his life-long friend Dick could not be brave
So Dick that evo-poofer sadly slipped in to his cave

Oh Poof the Magic Mutant, a-t-g-c
And changed them just by randomness just to see what he could be

Poof the Magic Mutant, a-t-g-c
And changed them just by randomness just to see what he could be

Naturalist use the poof concept all the time. They don’t say the actual word “poof,” they say “emerge.” It means the same thing. Something just came into existence which we cannot explain. It poofs or it emerges. Same-same.

What do you think Behe, Axe, Durston and others are doing? And believe me, they are scientists, whatever you may think.

However, many possible developments of ID theory do depend on the general research in biology, whoever is doing it. Facts are facts. IMO, all good biological research is ID research. It is the duty of ID theorists to interpret facts from general research in the light of ID theory. That’s what they do.

‘…. but it is undeniably an area of continuing research with hypotheses and data subject to refutation and confirmation i.e. science.

On the contrary it is only a slight variant of the much cited definition of madness: in this case, pursuing a blinkered approach to research on the basis of the groundless assumption of materialism, and expecting it to bear fruit. Arguably, even, in the circumstances, to ‘poof fruit’, if that’s not overloading the ambiguous imagery.

Admit it, Mark: You’re into scientism in a big way, making an idol of a paradigm based on a spurious hypothesis, a priori considering it more scientific than ID. I just hope you are not employed in an area which owes nothing to quantum mechanics or biomimetics.

Though the former is perhaps impossible today, biomimetics, with the reverse engineering it undertakes, has screamed intelligent design from the dawn of history to the unswerving conviction of the final, great scientific paradigm-changers’, namely, the giants of maths and physics of the early-to-middle part of the last century. And that, without an inkling if what is currently known about the sublime engineering, scale and beauty of the simplest cell, for example.

‘Self-organisation’ needs an explanation for why chaos should produce order, the absolute converse of the Christian axiom, that it falls to us to create order out of chaos, in imitation of the creator. I believe I read earlier today some minuscule, half-baked example of order emerging from chaos, immediately ‘shot down in flames’ as to trivial to count.

Mung, no one is saying sequences randomly assemble out of thin air except your friend Alan here. I am saying that when the paper refers to “de novo” generation of genes, it means they arise from noncoding stretches of DNA that are already there, but are not currently expressed as protein. Scordova and Alan would obviously like you to think that scientists say these sequences are just “poofing” out of nowhere, but they were there the whole time as noncoding sequences. I suggest you start getting your science info from a reputable source (not here).

I am saying that when the paper refers to “de novo” generation of genes, it means they arise from noncoding stretches of DNA that are already there, but are not currently expressed as protein.

Yes, I understand that is what you were saying.

Alan, otoh, assures us that’s not the way evolution works. He claims that “Evolution takes functional proteins and tries minor variations..”

He is contradicting you. He probably didn’t bother to read your post or did not understand it. I was just trying to bring it to his attention.

His statement that “It [evolution] does not randonmly assemble sequences from thin air” is a straw-man.

You statement that “no one is saying sequences randomly assemble out of thin air except your friend Alan here” demonstrates that your reading comprehension is right up there with Alan’s.

Are we having fun yet?

…but they were there the whole time as noncoding sequences.

No, they weren’t. They arose from non-coding sequences, according to your source. They weren’t just “always there” as noncoding sequences.

Your claim is contradicted by your own source. Did you even bother to read it?

The de novo evolution of genes out of random sequences has become a realistic possibility and this develops into the major model for orphan gene evolution (Siepel, 2009; Bornberg-Bauer et al., 2010; Tautz and Domazet-Loso, 2011).

This model posits that a new gene starts from
an initially spuriously transcribed genome regionthat acquires some additional mutations to convert the resulting ribonucleic acid (RNA) into a stable heritable
transcript…

Sheesh.

Note that the sequence is transcribed.

So much for the objection raised by wd400 (or was it franklin), who also seems to have not bothered to read the paper.

The first, fundamental problem is to identify when and where an irrefutable design implementation took place.

That is exactly what ID is trying to do at present.

Durston’s work on protein families has identified many structures for which a reliable design inference can and should be made.

Axe and Behe have done much to fix the level at which a design inference is necessary to explain the emergence of new protein structures.

Meyer has recently debated in detail the Cambrian explosion as a very well localized example of design implementation.

Identifying protein families or superfamilies as the basci unit of new design implementation will naturally give us a map of the inferable design activity in the course of natural history.

Many aspects of the “how” depend critically on the growing understanding of the emergence of new proteins. At present, we still don’t know if new proteins really emerge from non coding DNA, which would be a very reasonable assumption, or in other ways. If the non coding DNA hypothesis acquires support, a whole new scenario opens for detailed studies. ID is a much better framework for that than neo darwinism, which certainly cannot explain the transitions from random non functional sequences to ordered functional ones in cosmic times. If we don’t discard the irrational dogma that those transitions had to happen by RV + NS, we will never understand what really happened and how.

The deeper “how”, IOWs, how some conscious being could manipulate matter and input information in it, is certainly open to future scientific approach and discussion, but I think that at present that would be mere philosophy, until we have greater details about the previous points. The same is true for the deeper “why”, but obviously a lot of simpler “whys” are open to inquiry in an ID framework. For example, we can wonder why some protein family appears at some time in natural history, and try to explain or understand that in terms of its functional potentialities, instead of the old dogma of fitness advantage.

Whatever you can say, it is obvious that the acceptance, even if only as operative hypothesis, of the ID framework can give science a whole new way of looking at facts and interpreting them, helping us to get rid of an old and wrong paradigm which leads nowhere.

Of course AVS is correct. He is making a specific point about paper “the Evolutionary Origin of
Orphan Genes” linked in the OP. I was making a general point about how organisms stumble upon useful new proteins. In fact the paper supports this point most elegantly!

The simple point, however, is that functional proteins can never derive from non coding DNA by the neo darwinian mechanism of RV + NS. Design is the only reasonable explanation for such a transition.

Disagree with this assertion. When I am talking about a functional protein, I mean useful in some organism’s biochemistry in some circumstances. Orphan genes as a source of variation that can be selected for seems a most elegant demonstration of the power and breadth of evolutionary processes.

It appears that genomes harbour many transcripts in a transition stage from non-functional to functional genes, also known as protogenes, which are exposed to evolutionary testing and can become ?xed when they turn out to be useful.

It appears that genomes harbour many transcripts in a transition stage from nonfunctional to functional genes, also known as protogenes, which are exposed to evolutionary testing and can become fixed when they turn out to be useful.

And exactly what would this ‘evolutionary testing’ look like Mr. Fox? Would it be some type of environmental shift?

Here is a Completely Different Way of Doing Science – Cornelius Hunter PhD. – April 2012
Excerpt: But how then could evolution proceed if mutations were just neutral? The idea was that neutral mutations would accrue until finally an earthquake, comet, volcano or some such would cause a major environmental shift which suddenly could make use of all those neutral mutations. Suddenly, those old mutations went from goat-to-hero, providing just the designs that were needed to cope with the new environmental challenge. It was another example of the incredible serendipity that evolutionists call upon.
Too good to be true? Not for evolutionists. The neutral theory became quite popular in the literature. The idea that mutations were not brimming with cool innovations but were mostly bad or at best neutral, for some, went from an anathema to orthodoxy. And the idea that those neutral mutations would later magically provide the needed innovations became another evolutionary just-so story, told with conviction as though it was a scientific finding.
Another problem with the theory of neutral molecular evolution is that it made even more obvious the awkward question of where these genes came from in the first place.http://darwins-god.blogspot.co.....ay-of.html

Mr. Fox, if this is the type of imagined scenario you are envisioning, let me be the first to inform you that such imagined scenarios for ‘evolutionary testing fall far short of scientific proof.

Mr. Fox, but what would real, not imagined, ‘evolutionary testing’ really look like if random neo-Darwinian processes truly were looking for new proteins in sequence space???

Dr. Durston elaborates on how futile an evolutionary search is to find a single functional protein:
Excerpt: From this, we can come up with a very rough estimate for the total number of stable, folding 3D sequences in 300 residue sequence space … roughly 10^74 sequences that will give stable 3D folds (this is very rough, but it will illustrate my point and help one see why scientists don’t search for novel stable 3D folds from a library of random sequences). One might think that 10^75 sequences is an enormous number, however, it is miniscule in comparison with 20^300, which is the total number of sequences in 300 –residue sequence space. This is why the theory that an evolutionary search, even if it involved all the planets in all the galaxies of the known universe, is utterly implausible.http://www.uncommondescent.com.....ent-466489

Even using the atheists own overly optimistic number (one in a trillion) for finding functional proteins in sequence space revels the ludicrous nature of this imagined ‘evolutionary testing’ you are so smitten with Mr. Fox:

How Proteins Evolved – Cornelius Hunter – December 2010
Excerpt: Comparing ATP binding with the incredible feats of hemoglobin, for example, is like comparing a tricycle with a jet airplane. And even the one in 10^12 shot, though it pales in comparison to the odds of constructing a more useful protein machine, is no small barrier. If that is what is required to even achieve simple ATP binding, then evolution would need to be incessantly running unsuccessful trials. The machinery to construct, use and benefit from a potential protein product would have to be in place, while failure after failure results. Evolution would make Thomas Edison appear lazy, running millions of trials after millions of trials before finding even the tiniest of function.http://darwins-god.blogspot.co.....olved.html

Moreover, as if all of that was not bad enough for the notion of ‘evolutionary testing’, it is found that ribosomes are a stickler for protein fidelity that precludes any such ‘evolutionary testing’ scenario from being realistic:

The Ribosome: Perfectionist Protein-maker Trashes Errors
Excerpt: The enzyme machine that translates a cell’s DNA code into the proteins of life is nothing if not an editorial perfectionist…the ribosome exerts far tighter quality control than anyone ever suspected over its precious protein products… To their further surprise, the ribosome lets go of error-laden proteins 10,000 times faster than it would normally release error-free proteins, a rate of destruction that Green says is “shocking” and reveals just how much of a stickler the ribosome is about high-fidelity protein synthesis.http://www.sciencedaily.com/re.....134529.htm

And exactly how is the evolution new life forms suppose to ‘randomly’ occur if it is prevented from ‘randomly’ occurring to the proteins in the first place?

Moreover Mr. Fox, as if all that wasn’t bad enough for your preferred Darwinian worldview, it is now found that many ORFans are deeply embedded in the genome and are not recent evolutionary add ons:

Age doesn’t matter: New genes are as essential as ancient ones – December 2010
Excerpt: “A new gene is as essential as any other gene; the importance of a gene is independent of its age,” said Manyuan Long, PhD, Professor of Ecology & Evolution and senior author of the paper. “New genes are no longer just vinegar, they are now equally likely to be butter and bread. We were shocked.”http://www.sciencedaily.com/re.....142523.htm

This finding is particularly troublesome for your imagined ‘evolutionary testing’ scenario since ORFans deeply embedded in genomes presents its own unique set of insurmountable difficulties for Darwinists:

Darwin or Design? – Paul Nelson at Saddleback Church – Nov. 2012 – ontogenetic depth (excellent update) – video
Text from one of the Saddleback slides:
1. Animal body plans are built in each generation by a stepwise process, from the fertilized egg to the many cells of the adult. The earliest stages in this process determine what follows.
2. Thus, to change — that is, to evolve — any body plan, mutations expressed early in development must occur, be viable, and be stably transmitted to offspring.
3. But such early-acting mutations of global effect are those least likely to be tolerated by the embryo.
Losses of structures are the only exception to this otherwise universal generalization about animal development and evolution. Many species will tolerate phenotypic losses if their local (environmental) circumstances are favorable. Hence island or cave fauna often lose (for instance) wings or eyes.http://www.saddleback.com/mc/m/7ece8/

Needless to say, none of this is good for your imagined ‘evolutionary testing’ conjecture that you have placed your ill-founded hope in Mr. Fox!

Dr. Axe challenges a Darwinist to create a single new gene by Darwinian processes:
Show Me: A Challenge for Martin Poenie – Douglas Axe August 16, 2013
Excerpt: Poenie want to be free to appeal to evolutionary processes for explaining past events without shouldering any responsibility for demonstrating that these processes actually work in the present. That clearly isn’t valid. Unless we want to rewrite the rules of science, we have to assume that what doesn’t work didn’t work.
It isn’t valid to think that evolution did create new enzymes if it hasn’t been demonstrated that it can create new enzymes. And if Poenie really thinks this has been done, then I’d like to present him with an opportunity to prove it. He says, “Recombination can do all the things that Axe thinks are impossible.” Can it really? Please show me, Martin!
I’ll send you a strain of E. coli that lacks the bioF gene, and you show me how recombination, or any other natural process operating in that strain, can create a new gene that does the job of bioF within a few billion years.http://www.evolutionnews.org/2.....75611.html